So if I understand it right it can be rendered in two ways?
In my lines style, add a rule waterway=canal & mkgmap:wayclosed=true {add natural=water}
Or
Use the continue in the line style after each waterway that needs to be processed and in the polygon style add a rule:
waterway=canal & mkgmap:autoclosing=false [0x3c resolution 22]
I used the last one and got a few severe styledconverter warnings: Use line rules only for way#
A few more tests: The first method, adding natural=water to waterway=canal & mkgmap:wayclosed=true in my line style didn't work. Only the last method (mkgmap:autoclosing=false in my polygons style) worked. And btw I got not just a few warnings, they were a lot, it looked like those warnings were printed for every single highway (even when I didnt process them, I just tested a map with only water styles)